Cows’ milk allergy is the most common infant food allergy, requiring a strict exclusion diet usually for the first year of life. This exclusion of a main food group occurs at a critical time in the development of food preferences and eating habits. It is known that infants are born with an innate predisposition to prefer and reject certain tastes. However, these innate preferences can be altered with exposure to (and exclusion of) different foods. The aim of this research was to determine if the use of substitute formula and exclusion of milk products in the management of cows’ milk allergy affects fussy eating and food preferences in the short or long term. This research consisted of two separate cross-sectional studies that measured eating behaviours in children currently and previously consuming an exclusion diet for cows’ milk allergy. Two different age groups were assessed; infants and school-aged children. The outcome measures were: fussy eating, food neophobia, feeding difficulties, dietary variety, nutritional intake, food preference, taste preference and growth. The main findings were that children currently consuming an exclusion diet for cows’ milk allergy have higher levels of fussy eating, feeding difficulties and food neophobia compared to a control group. These levels were associated with the number and type of allergic symptoms. Children who had consumed an exclusion diet for cows’ milk allergy in infancy had significantly higher levels of avoidant eating behaviour and a lower preference for dairy products than the control group, several years after cows’ milk had been reintroduced. Significant differences in dietary variety and the intake of some micronutrients were observed, but there was no difference in growth measurements between groups at either age. This research has identified some novel findings, which have implications for health professionals and researchers working in food allergy and childhood nutrition. Whilst consuming an exclusion diet is essential for symptomatic relief in the management of cows’ milk allergy, it is clear that it can have secondary effects on fussy eating and food preferences. These secondary effects can persist into adolescence. It therefore underlines the importance of ensuring exclusion diets for food allergy are not initiated unnecessarily or implemented for too long. The diagnosis of cows’ milk allergy needs to be robust and monitoring of both exclusion diets and fussy eating should be timely.